@graphty/algorithms 2.1.1 → 2.2.0

package/dist/src/indexed/label-propagation.js

@@ -0,0 +1,486 @@
+import { INVALID_INDEX, renumberPartition, } from "@graphty/graph-format";
+import { withGroups } from "./components.js";
+/** Epochs run 0 .. EPOCH_LIMIT - 1 between resets of the Int32 stamp arrays. */
+const EPOCH_LIMIT = 0x7fffffff;
+/**
+ * mulberry32: 32-bit state, output in [0, 1). The exact sequence is part of the result contract
+ * (design section 2.4): changing it changes every partition.
+ * @param seed - Generator seed; only its low 32 bits are used
+ * @returns The generator
+ */
+export function mulberry32(seed) {
+    let a = seed >>> 0;
+    return () => {
+        a = (a + 0x6d2b79f5) | 0;
+        let t = Math.imul(a ^ (a >>> 15), 1 | a);
+        t = (t + Math.imul(t ^ (t >>> 7), 61 | t)) ^ t;
+        return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+    };
+}
+/**
+ * Whether any arc other than a self-loop carries a positive vote under the chosen weighting, which
+ * is exactly when the identity labelling is NOT dominant everywhere.
+ * @param s - The snapshot
+ * @param weights - The arc weights in use, or null when every arc votes 1
+ * @returns True when some node has a positive-weight neighbour
+ */
+function hasVotingArc(s, weights) {
+    for (let u = 0; u < s.nodeCount; u++) {
+        const end = s.rowPtr[u + 1];
+        for (let a = s.rowPtr[u]; a < end; a++) {
+            if (s.colIdx[a] !== u && (weights === null || weights[a] > 0)) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+/**
+ * Whether every node not held fixed holds a label at the largest vote among its neighbours (or has
+ * no neighbour that votes).
+ * @param tally - A tally over the voting rows
+ * @param label - The label of every node
+ * @param fixed - 1 for a node held at its label, or null when none is
+ * @returns True when no free node would move
+ */
+function allDominant(tally, label, fixed) {
+    for (let u = 0; u < label.length; u++) {
+        if (fixed !== null && fixed[u] === 1) {
+            continue;
+        }
+        const max = tally.collect(u, label);
+        if (max !== 0 && tally.voteOf(label[u]) !== max) {
+            return false;
+        }
+    }
+    return true;
+}
+/**
+ * The per-arc weights of `view` that the votes use: the snapshot's exact f64 weights when it keeps
+ * them (graph-format keeps a role-"weight" f64 edge column whenever some weight is not f32-exact),
+ * gathered through arcToEdge; otherwise the view's own f32 arc array. Voting on the f32 values would
+ * turn 1 and 1 + 1e-9 into a tie, 1e39 into Infinity and 1e-50 into 0.
+ * @param view - The forward snapshot or its reverse view
+ * @param exact - The exact per-edge weights, or null when the f32 arc array is exact
+ * @returns The arc weights, or null when every arc weighs 1
+ */
+export function arcWeightsOf(view, exact) {
+    if (exact === null) {
+        return view.weights;
+    }
+    const out = new Float64Array(view.arcCount);
+    for (let a = 0; a < out.length; a++) {
+        out[a] = exact[view.arcToEdge[a]];
+    }
+    return out;
+}
+/**
+ * The exact per-edge weights of `s`: its role-"weight" f64 edge column when it keeps one, else null
+ * (the f32 arc array is then exact).
+ * @param s - The snapshot
+ * @returns The exact weights per logical edge, or null
+ */
+export function exactEdgeWeights(s) {
+    const shadow = s.edges.byRole("weight");
+    return shadow !== null && shadow.dtype === "f64" ? shadow.data : null;
+}
+/**
+ * Gather the voting rows of `s` and reject weights a vote cannot use.
+ * @param s - The snapshot
+ * @param weighted - Sum arc weights (true) or count each arc as 1 (false)
+ * @returns The rows and their weights
+ * @throws RangeError when a weight is negative, NaN or infinite
+ */
+function votingRows(s, weighted) {
+    const weights = weighted ? arcWeightsOf(s, exactEdgeWeights(s)) : null;
+    if (weights !== null) {
+        for (let a = 0; a < weights.length; a++) {
+            const w = weights[a];
+            if (!(w >= 0) || w === Infinity) {
+                throw new RangeError(`arc ${a} has weight ${w}; label propagation needs finite, non-negative weights`);
+            }
+        }
+    }
+    const rev = s.directed ? s.reverse() : null;
+    return {
+        sides: rev === null ? 1 : 2,
+        rowPtrs: [s.rowPtr, rev === null ? s.rowPtr : rev.rowPtr],
+        colIdxs: [s.colIdx, rev === null ? s.colIdx : rev.colIdx],
+        arcWeights: [weights, weights === null || rev === null ? weights : arcWeightsOf(rev, exactEdgeWeights(s))],
+        weights,
+    };
+}
+/**
+ * Check the options every label propagation shares.
+ * @param n - The node count
+ * @param maxIterations - The work cap
+ * @param randomSeed - The seed, or null when the variant takes none
+ * @throws RangeError for a bad option
+ */
+function checkOptions(n, maxIterations, randomSeed) {
+    if (!Number.isInteger(maxIterations) || maxIterations < 0) {
+        throw new RangeError(`maxIterations must be a non-negative integer, got ${maxIterations}`);
+    }
+    if (randomSeed !== null && !Number.isInteger(randomSeed)) {
+        throw new RangeError(`randomSeed must be a finite integer, got ${randomSeed}`);
+    }
+    if (maxIterations * n > Number.MAX_SAFE_INTEGER) {
+        throw new RangeError(`maxIterations * nodeCount (${maxIterations} * ${n}) exceeds Number.MAX_SAFE_INTEGER`);
+    }
+}
+/**
+ * The per-node vote tally shared by the queue kernel and the synchronous passes: an accumulator
+ * per label, stamped by visit so it never needs clearing.
+ */
+class Tally {
+    constructor(n, rows, weighted) {
+        this.rows = rows;
+        this.epoch = -1;
+        this.count = 0;
+        this.acc = new Float64Array(n);
+        this.stamp = new Int32Array(n).fill(-1);
+        this.touched = new Uint32Array(n);
+        this.seen = weighted ? null : new Int32Array(n).fill(-1);
+    }
+    /**
+     * Sum the votes of u's neighbours per label into `acc`, listing the labels met in `touched`.
+     * @param u - The node
+     * @param label - The label of every node
+     * @returns The largest vote, 0 when no neighbour votes
+     */
+    collect(u, label) {
+        if (++this.epoch === EPOCH_LIMIT) {
+            // Reset before the epoch leaves the Int32 range: O(n) once per 2^31 - 1 visits.
+            this.stamp.fill(-1);
+            this.seen?.fill(-1);
+            this.epoch = 0;
+        }
+        const { acc, stamp, touched, seen, rows } = this;
+        const visit = this.epoch;
+        let count = 0;
+        for (let side = 0; side < rows.sides; side++) {
+            const rowPtr = rows.rowPtrs[side];
+            const colIdx = rows.colIdxs[side];
+            const w = rows.arcWeights[side];
+            const end = rowPtr[u + 1];
+            for (let a = rowPtr[u]; a < end; a++) {
+                const v = colIdx[a];
+                if (v === u) {
+                    continue; // a self-loop does not vote
+                }
+                if (seen !== null) {
+                    if (seen[v] === visit) {
+                        continue;
+                    }
+                    seen[v] = visit;
+                }
+                const c = label[v];
+                const vote = w === null ? 1 : w[a];
+                if (stamp[c] !== visit) {
+                    stamp[c] = visit;
+                    acc[c] = vote;
+                    touched[count++] = c;
+                }
+                else {
+                    acc[c] += vote;
+                }
+            }
+        }
+        this.count = count;
+        let max = 0;
+        for (let i = 0; i < count; i++) {
+            if (acc[touched[i]] > max) {
+                max = acc[touched[i]];
+            }
+        }
+        return max;
+    }
+    /**
+     * The vote label c received in the last `collect`.
+     * @param c - A label
+     * @returns Its vote, 0 when no neighbour holds it
+     */
+    voteOf(c) {
+        return this.stamp[c] === this.epoch ? this.acc[c] : 0;
+    }
+}
+/**
+ * The FLPA queue kernel over `label`, updated in place. Nodes marked in `fixed` never enter the
+ * queue, so they keep their starting label.
+ * @param s - The snapshot
+ * @param rows - Its voting rows
+ * @param weighted - Whether the rows carry weights
+ * @param label - Starting label of every node, each below nodeCount; overwritten with the result
+ * @param fixed - 1 for a node whose label never changes, or null
+ * @param maxIterations - Work cap in node visits per node
+ * @param randomSeed - Seed of the visit order and the tie draws
+ * @returns The node visits run and the nodes still queued
+ */
+function flpa(s, rows, weighted, label, fixed, maxIterations, randomSeed) {
+    const n = s.nodeCount;
+    const rand = mulberry32(randomSeed);
+    const tally = new Tally(n, rows, weighted);
+    // A ring of n + 1 slots: `queued` keeps a node in it at most once.
+    const capacity = n + 1;
+    const queue = new Uint32Array(capacity);
+    const queued = new Uint8Array(n);
+    let size = 0;
+    for (let i = 0; i < n; i++) {
+        if (fixed === null || fixed[i] === 0) {
+            queue[size++] = i;
+            queued[i] = 1;
+        }
+    }
+    for (let i = size - 1; i >= 1; i--) {
+        const j = Math.floor(rand() * (i + 1));
+        const t = queue[i];
+        queue[i] = queue[j];
+        queue[j] = t;
+    }
+    let head = 0;
+    let tail = size;
+    const maxVisits = maxIterations * n;
+    let visits = 0;
+    const { touched, acc } = tally;
+    while (size > 0 && visits < maxVisits) {
+        const u = queue[head];
+        head = head + 1 === capacity ? 0 : head + 1;
+        size--;
+        queued[u] = 0;
+        visits++;
+        const max = tally.collect(u, label);
+        if (max === 0) {
+            continue; // no positive-weight neighbour: keep the label
+        }
+        // Reservoir draw over the labels at the maximum: the k-th replaces the pick with
+        // probability 1/k, so a single dominant label consumes no random number.
+        let pick = 0;
+        let tied = 0;
+        for (let i = 0; i < tally.count; i++) {
+            const c = touched[i];
+            if (acc[c] === max) {
+                tied++;
+                if (tied === 1 || rand() * tied < 1) {
+                    pick = c;
+                }
+            }
+        }
+        if (pick === label[u]) {
+            continue;
+        }
+        label[u] = pick;
+        // A neighbour already holding the new label can only have been strengthened by the move.
+        // Both rows, so on a directed snapshot the nodes that read u are requeued too.
+        for (let side = 0; side < rows.sides; side++) {
+            const rowPtr = rows.rowPtrs[side];
+            const colIdx = rows.colIdxs[side];
+            const end = rowPtr[u + 1];
+            for (let a = rowPtr[u]; a < end; a++) {
+                const v = colIdx[a];
+                if (queued[v] === 0 && label[v] !== pick && (fixed === null || fixed[v] === 0)) {
+                    queued[v] = 1;
+                    queue[tail] = v;
+                    tail = tail + 1 === capacity ? 0 : tail + 1;
+                    size++;
+                }
+            }
+        }
+    }
+    return { visits, size };
+}
+/**
+ * Community detection by fast label propagation (FLPA; Traag and Subelj, Sci. Rep. 13:2701, 2023,
+ * Algorithm 3), the queue-driven form of Raghavan, Albert and Kumara's asynchronous label
+ * propagation.
+ *
+ * Every node starts in its own community. Nodes are visited from a queue that starts as a seeded
+ * shuffle of all of them; a visited node adopts the label with the largest summed arc weight among
+ * its neighbours, drawing uniformly at random among tied labels (its current label included, with
+ * no priority). When its label changes, every neighbour holding a different label is queued again.
+ * The run ends when the queue empties -- then every node's label is dominant among its neighbours
+ * and `converged` is true -- or after `maxIterations * nodeCount` node visits.
+ *
+ * Conventions: self-loops are skipped; parallel arcs are summed; on a directed snapshot a node's
+ * neighbours are its out-arcs AND its in-arcs, so a reciprocal pair counts twice. With
+ * `weighted: false` each distinct neighbour votes once. A negative, NaN or infinite weight throws.
+ * Votes use the exact f64 weights when the snapshot keeps them (as `toSnapshot` does for a legacy
+ * graph whose weights are not all f32-exact), so a weight rounded in the f32 arc array never
+ * decides a vote.
+ *
+ * One `randomSeed` gives one result, bit for bit. The partitions differ from the legacy
+ * `labelPropagation` for the same seed: the random stream and the stop rule are different
+ * (design `design/algorithms/label-propagation-indexed-port-design.md`, section 3).
+ * @param s - Any snapshot
+ * @param options - Work cap, seed and weighting
+ * @returns The partition, the full-sweep equivalents run, and whether the work queue emptied
+ * @public
+ */
+export function labelPropagation(s, options = {}) {
+    const maxIterations = options.maxIterations ?? 100;
+    const randomSeed = options.randomSeed ?? 42;
+    const weighted = options.weighted ?? true;
+    const n = s.nodeCount;
+    checkOptions(n, maxIterations, randomSeed);
+    const rows = votingRows(s, weighted);
+    const label = new Uint32Array(n);
+    for (let i = 0; i < n; i++) {
+        label[i] = i;
+    }
+    if (n === 0 || maxIterations === 0) {
+        const { labels, count } = renumberPartition(label);
+        return { ...withGroups(labels, count), iterations: 0, converged: !hasVotingArc(s, rows.weights) };
+    }
+    const { visits, size } = flpa(s, rows, weighted, label, null, maxIterations, randomSeed);
+    const { labels, count } = renumberPartition(label);
+    return { ...withGroups(labels, count), iterations: Math.ceil(visits / n), converged: size === 0 };
+}
+/**
+ * Semi-supervised label propagation: the FLPA kernel of {@link labelPropagation} with some nodes
+ * held at a given label (the `initial` / `fixed` inputs of igraph's `community_label_propagation`).
+ *
+ * A seeded node keeps its label for the whole run and is never visited; every other node starts in
+ * its own community and moves as in `labelPropagation`. Seeds that share a label share one community
+ * from the start, and seeds with different labels are never merged, so in the result two seeds
+ * carry the same label exactly when their seed labels are equal. The result is renumbered to
+ * `0..count-1` in first-seen node order like every other partition here, so a seed label's VALUE is
+ * not kept: read a seed's community through `labels[seedNode]`. With no seed at all this is
+ * `labelPropagation` with the same seed and options, bit for bit.
+ *
+ * `converged` is true when the work queue emptied, or when `maxIterations` is 0 and the starting
+ * labels already are dominant: every unseeded node's label is dominant among its neighbours.
+ * Seeded nodes are not held to that.
+ * @param s - Any snapshot
+ * @param seeds - One entry per node: its fixed label, any value but `INVALID_INDEX`, or
+ *   `INVALID_INDEX` for a node free to move
+ * @param options - Work cap, seed of the visit order and weighting
+ * @returns The partition, the full-sweep equivalents run, and whether the work queue emptied
+ * @throws RangeError when `seeds` is not one entry per node, or for a bad option or weight
+ * @public
+ */
+export function labelPropagationSemiSupervised(s, seeds, options = {}) {
+    const maxIterations = options.maxIterations ?? 100;
+    const randomSeed = options.randomSeed ?? 42;
+    const weighted = options.weighted ?? true;
+    const n = s.nodeCount;
+    if (seeds.length !== n) {
+        throw new RangeError(`seeds has ${seeds.length} entries; the snapshot has ${n} nodes`);
+    }
+    checkOptions(n, maxIterations, randomSeed);
+    const rows = votingRows(s, weighted);
+    // The kernel's labels are node indices, so a seed label becomes the index of the first node
+    // seeded with it: a free node's own index can never collide with it.
+    const label = new Uint32Array(n);
+    const fixed = new Uint8Array(n);
+    const firstWith = new Map();
+    for (let u = 0; u < n; u++) {
+        const seed = seeds[u];
+        if (seed === INVALID_INDEX) {
+            label[u] = u;
+            continue;
+        }
+        let first = firstWith.get(seed);
+        if (first === undefined) {
+            first = u;
+            firstWith.set(seed, u);
+        }
+        label[u] = first;
+        fixed[u] = 1;
+    }
+    const { visits, size } = flpa(s, rows, weighted, label, fixed, maxIterations, randomSeed);
+    // At maxIterations 0 nothing was visited, so the queue says nothing: check the labels, as
+    // labelPropagation does.
+    const converged = size === 0 || (maxIterations === 0 && allDominant(new Tally(n, rows, weighted), label, fixed));
+    const { labels, count } = renumberPartition(label);
+    return { ...withGroups(labels, count), iterations: n === 0 ? 0 : Math.ceil(visits / n), converged };
+}
+/**
+ * Label propagation in synchronous passes: every node reads its neighbours' labels from the
+ * previous pass, and all nodes move at once. Deterministic, with no random stream.
+ *
+ * A node keeps its label when that label is dominant among its neighbours; otherwise it takes the
+ * LOWEST label with the largest summed vote. Synchronous updates alone make two neighbours trade
+ * labels for ever (on a single edge a-b, a takes b's label while b takes a's), so passes alternate
+ * a swap guard: an even pass (the first is pass 0) lets a node move only to a higher label, an odd
+ * pass only to a lower one (the up/down rule of cuGraph's Louvain move phase). The run stops after
+ * two passes in a row with no move, one up and one down -- then every node's label is dominant and
+ * `converged` is true -- or after `maxIterations` passes.
+ *
+ * The guard stops the single-edge swap but not every cycle: on some weighted graphs a node climbs to
+ * a higher label on each up pass and falls back on each down pass. When a pass returns the labels
+ * of two passes before, the run can only repeat itself, so it stops there with `converged` false;
+ * the result is then the same for any larger `maxIterations`. Longer cycles run to the cap.
+ *
+ * This is what the legacy `labelPropagationAsync` does, despite its name, with the swap guard it
+ * lacks and the tie rule applied to the finished tally rather than to a running one. Conventions
+ * match {@link labelPropagation}: self-loops are skipped, parallel arcs summed, a directed snapshot
+ * reads out- and in-neighbours, weights are the exact f64 ones when the snapshot keeps them, and a
+ * negative, NaN or infinite weight throws.
+ * @param s - Any snapshot
+ * @param options - Pass cap and weighting
+ * @returns The partition, the passes run, and whether every label ended dominant
+ * @public
+ */
+export function labelPropagationSynchronous(s, options = {}) {
+    const maxIterations = options.maxIterations ?? 100;
+    const weighted = options.weighted ?? true;
+    const n = s.nodeCount;
+    checkOptions(n, maxIterations, null);
+    const rows = votingRows(s, weighted);
+    const tally = new Tally(n, rows, weighted);
+    const { touched, acc } = tally;
+    let label = new Uint32Array(n);
+    let next = new Uint32Array(n);
+    // The labels two passes back, to catch a period-2 cycle.
+    let before = new Uint32Array(n).fill(INVALID_INDEX);
+    for (let i = 0; i < n; i++) {
+        label[i] = i;
+    }
+    let passes = 0;
+    let quiet = 0;
+    let cycling = false;
+    while (quiet < 2 && passes < maxIterations && !cycling) {
+        const up = passes % 2 === 0;
+        passes++;
+        let moved = false;
+        for (let u = 0; u < n; u++) {
+            const current = label[u];
+            next[u] = current;
+            const max = tally.collect(u, label);
+            if (max === 0 || tally.voteOf(current) === max) {
+                continue;
+            }
+            let best = INVALID_INDEX;
+            for (let i = 0; i < tally.count; i++) {
+                const c = touched[i];
+                if (acc[c] === max && c < best) {
+                    best = c;
+                }
+            }
+            if (up ? best > current : best < current) {
+                next[u] = best;
+                moved = true;
+            }
+        }
+        cycling = moved && sameLabels(next, before);
+        [before, label, next] = [label, next, before];
+        quiet = moved ? 0 : quiet + 1;
+    }
+    const converged = quiet >= 2 || allDominant(tally, label, null);
+    const { labels, count } = renumberPartition(label);
+    return { ...withGroups(labels, count), iterations: passes, converged };
+}
+/**
+ * Whether two label arrays are equal.
+ * @param a - Labels
+ * @param b - Labels of the same length
+ * @returns True when every entry matches
+ */
+function sameLabels(a, b) {
+    for (let i = 0; i < a.length; i++) {
+        if (a[i] !== b[i]) {
+            return false;
+        }
+    }
+    return true;
+}
+//# sourceMappingURL=label-propagation.js.map

package/dist/src/indexed/label-propagation.js.map

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package/dist/src/indexed/leiden.d.ts

@@ -0,0 +1,52 @@
+import { type GraphSnapshot } from "@graphty/graph-format";
+import { type LabelResult } from "./components.js";
+/**
+ * Options of the index-based Leiden. The names and defaults are the legacy `leiden`'s, but
+ * `maxIterations` counts something else: see below.
+ * @public
+ */
+export interface LeidenOptions {
+    /** Resolution gamma: above 1 favours smaller communities; default 1. */
+    readonly resolution?: number | undefined;
+    /** Seed of the visit orders; default 42. */
+    readonly randomSeed?: number | undefined;
+    /**
+     * Cap on whole passes over the original graph, each running as many levels as it needs; default
+     * 100. The legacy `leiden` caps levels instead, so its `maxIterations: 1` is one level where
+     * this is one full pass. The result's `iterations` counts levels.
+     */
+    readonly maxIterations?: number | undefined;
+    /** Stop once a pass improves modularity by no more than this; default 1e-7. */
+    readonly threshold?: number | undefined;
+}
+/** Result of the index-based Leiden: a partition plus the modularity it reaches. @public */
+export interface LeidenResult extends LabelResult {
+    /** Modularity of the returned partition, at the requested resolution. */
+    readonly modularity: number;
+    /** Levels processed, summed over every pass. */
+    readonly iterations: number;
+}
+/**
+ * Leiden community detection (Traag, Waltman and van Eck, Sci. Rep. 9:5233, 2019) over an
+ * undirected snapshot: fast local moving, refinement into well-connected sub-communities, and
+ * aggregation by `contract()` once per level. Whole passes repeat from the previous answer, keeping
+ * a pass only when it raises modularity, until three passes in a row improve it by no more than
+ * `threshold` or `maxIterations` passes have run; every pass starts by moving single original
+ * nodes, so the answer is also a local optimum of those moves.
+ *
+ * Modularity follows graph-format's `weightedDegree()` convention (a self-loop counts twice), which
+ * on a graph without self-loops equals the legacy `leiden`'s. Weights are the exact f64 ones when
+ * the snapshot keeps them. The partition is not the legacy function's move for move: the legacy
+ * `leiden` splits disconnected communities rather than refining them, and visits nodes in another
+ * order; what this guarantees is connected communities. Both are randomised heuristics, so for one
+ * seed either can come out ahead; on the shared fixtures this one's modularity is at least the
+ * legacy's at the default seed and on average over seeds.
+ * @param s - An undirected snapshot
+ * @param options - Resolution, seed, pass cap and stopping threshold
+ * @returns The partition, its modularity, and the levels processed
+ * @throws Error on a directed snapshot; RangeError for a negative, NaN or infinite weight or a
+ *   fractional seed
+ * @public
+ */
+export declare function leiden(s: GraphSnapshot, options?: LeidenOptions): LeidenResult;
+//# sourceMappingURL=leiden.d.ts.map

package/dist/src/indexed/leiden.d.ts.map

@@ -0,0 +1 @@
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